run over that spot again with the weight brush, multiple bones can have the same color assigned to them, making it look like the area is connected to the right bone, when its actually connected to a different bone nowhere near it.

It pays to model legs/feet a little bit apart, for easier skinning. Chances are you're accidentally catching a point on the other heel/foot. Use arc rotate and get to an angle where theres nothiong behind the part you're skinning. (and change size of brush if you need to. ((Build -> weight brush)). I can get most trickier stuff done with a size 12, and weight of between 0.8 and 1)

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multiple bones can have the same color assigned to them, making it look like the area is connected to the right bone, when its actually connected to a different bone nowhere near it.

Very true Smirkyguy . (Hopefully one day we'll get some more colours.)